What is the likelihood of the IRS coming after her assets (including the branches) to cover their losses?

Once the criminal matter is resolved they'll resume collection activity. (Once a case is accepted for development of a criminal case they stop all civil collection efforts.) I don't know what type of entity owns the business, but assuming it's a corporation, they look first to corporate assets. If they can't collect in full there they turn to the responsible persons in the business. If they had enough evidence against her for a criminal case you can be sure they have enough evidence to assess the unpaid withheld taxes against her and pursue her assets.

Who is imposing the jail and fine? Not the IRS, right? Will there be an attempt to collect that money?

Criminal penalties, including the fine that was mentioned, are imposed by the courts. I believe the US Marshall's office deals with things like payment of fines.

Sometimes probation orders will include a requirement to pay the civil liability as well as any fines.

One of the statements in the DA's release:

“Employers who commit Employment Tax Fraud by failing to remit employment taxes are not only defrauding the United States government, they are creating financial havoc for their employees,” said Stephen Boyd, Special Agent in Charge, IRS Criminal Investigation, Denver Field Office.